@jbrowse/plugin-bed 5.0.0-beta.3 → 5.0.0-beta.7

package/esm/BedAdapter/configSchema.js

@@ -1,7 +1,9 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, fillLocations } from '@jbrowse/core/configuration';
 export function normalizeSnapshot(snap) {
     return snap.uri
-        ? { ...snap, bedLocation: { uri: snap.uri, baseUri: snap.baseUri } }
+        ? fillLocations(snap, {
+            bedLocation: { uri: snap.uri, baseUri: snap.baseUri },
+        })
         : snap;
 }
 /**

package/esm/BedGraphAdapter/configSchema.js

@@ -1,13 +1,12 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, fillLocations } from '@jbrowse/core/configuration';
 export function normalizeSnapshot(snap) {
     return snap.uri
-        ? {
-            ...snap,
+        ? fillLocations(snap, {
             bedGraphLocation: {
                 uri: snap.uri,
                 baseUri: snap.baseUri,
             },
-        }
+        })
         : snap;
 }
 /**

package/esm/BedpeAdapter/configSchema.js

@@ -1,14 +1,13 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, fillLocations } from '@jbrowse/core/configuration';
 export function normalizeSnapshot(snap) {
     return snap.uri
-        ? {
-            ...snap,
+        ? fillLocations(snap, {
             bedpeLocation: {
                 uri: snap.uri,
                 baseUri: snap.baseUri,
                 locationType: 'UriLocation',
             },
-        }
+        })
         : snap;
 }
 /**

package/esm/BigBedAdapter/configSchema.js

@@ -1,14 +1,13 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, fillLocations } from '@jbrowse/core/configuration';
 import { densityAdapterConfigSchemaFields } from '@jbrowse/core/data_adapters/BaseAdapter';
 export function normalizeSnapshot(snap) {
     return snap.uri
-        ? {
-            ...snap,
+        ? fillLocations(snap, {
             bigBedLocation: {
                 uri: snap.uri,
                 baseUri: snap.baseUri,
             },
-        }
+        })
         : snap;
 }
 /**

package/esm/StarFusionAdapter/StarFusionAdapter.js

@@ -2,42 +2,9 @@ import { BaseFeatureDataAdapter, cachedSetup, } from '@jbrowse/core/data_adapter
 import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
+import { parseStarFusionBreakpoint, starFusionColumns, } from '@jbrowse/core/util/starFusion';
 import { buildPairedIntervalTree, intervalTreeFeatures, } from '../adapterUtil.js';
-/**
- * A STAR-Fusion `refName:pos:strand` breakpoint, read from the RIGHT: a refName
- * may contain colons. GRCh38's full analysis set names its HLA contigs
- * `HLA-A*01:01:01:01`, so a breakpoint on one arrives as
- * `HLA-A*01:01:01:01:5000:+` and splitting at the first colon read the contig as
- * `HLA-A*01`, the position as 1 and the strand as absent. Same rule
- * `parseSvAlt` applies to a BND mate locstring, one field further along.
- *
- * A string with fewer than three fields keeps what it always parsed to, so a
- * truncated or strandless row is no worse off than before.
- */
-function parseBreakpoint(str) {
-    const parts = str.split(':');
-    const strandStr = parts.length >= 3 ? parts.pop() : undefined;
-    const pos = parts.length >= 2 ? +parts.pop() : Number.NaN;
-    return {
-        refName: parts.join(':'),
-        start: pos,
-        end: pos + 1,
-        strand: strandStr === '+' ? 1 : strandStr === '-' ? -1 : undefined,
-    };
-}
-/**
- * Which way the sequence a breakpoint keeps runs from it, as the paired-arc
- * display's mate-direction tick (1 = right, -1 = left, 0 = unknown). A
- * breakpoint's strand in STAR-Fusion is its gene's transcription strand, and the
- * fusion transcript keeps the donor's sequence 5' of the junction and the
- * acceptor's 3' of it: so on a + strand donor the retained side is at lower
- * coordinates and on a + strand acceptor it is at higher ones.
- */
-function tickDirection(strand, isDonor) {
-    return strand === undefined ? 0 : isDonor ? -strand : strand;
-}
 export default class StarFusionAdapter extends BaseFeatureDataAdapter {
-    // No `label`: `fetchAndMaybeUnzip` narrates the download from inside.
     loadData = cachedSetup({ setup: opts => this.loadDataP(opts) });
     intervalTrees = {};
     static capabilities = ['getFeatures', 'getRefNames'];
@@ -48,23 +15,19 @@ export default class StarFusionAdapter extends BaseFeatureDataAdapter {
         let rightIdx = -1;
         const feats1 = {};
         const feats2 = {};
-        parseLineByLine(buffer, line => {
-            if (line.startsWith('#')) {
-                columnNames = line.slice(1).split('\t');
+        parseLineByLine(buffer, (line, lineIndex) => {
+            if (lineIndex === 0) {
+                columnNames = starFusionColumns(line);
                 leftIdx = columnNames.indexOf('LeftBreakpoint');
                 rightIdx = columnNames.indexOf('RightBreakpoint');
             }
-            else if (leftIdx >= 0 && rightIdx >= 0) {
+            else if (!line.startsWith('#')) {
                 const cols = line.split('\t');
                 const left = cols[leftIdx];
                 const right = cols[rightIdx];
-                // through parseBreakpoint, so the bucket a row is filed under is the
-                // refName its feature will report -- a colon-bearing contig split two
-                // ways puts the row in a bucket no query can reach
-                const leftRef = left ? parseBreakpoint(left).refName : undefined;
-                const rightRef = right ? parseBreakpoint(right).refName : undefined;
-                if (leftRef && rightRef) {
-                    ;
+                if (left && right) {
+                    const leftRef = parseStarFusionBreakpoint(left, true).refName;
+                    const rightRef = parseStarFusionBreakpoint(right, false).refName;
                     (feats1[leftRef] ??= []).push(line);
                     (feats2[rightRef] ??= []).push(line);
                 }
@@ -80,27 +43,16 @@ export default class StarFusionAdapter extends BaseFeatureDataAdapter {
     featureFromLine(line, columnNames, uniqueId, flip) {
         const cols = line.split('\t');
         const row = Object.fromEntries(columnNames.map((name, i) => [name, cols[i]]));
-        const primaryBp = parseBreakpoint((flip ? row.RightBreakpoint : row.LeftBreakpoint));
-        const mateBp = parseBreakpoint((flip ? row.LeftBreakpoint : row.RightBreakpoint));
-        // the LeftBreakpoint is the donor, so this feature is the donor end of the
-        // junction whenever it is not flipped, and the mate is the other end
+        const donor = parseStarFusionBreakpoint(row.LeftBreakpoint, true);
+        const acceptor = parseStarFusionBreakpoint(row.RightBreakpoint, false);
+        const [primary, mate] = flip ? [acceptor, donor] : [donor, acceptor];
         return new SimpleFeature({
             uniqueId,
-            refName: primaryBp.refName,
-            start: primaryBp.start,
-            end: primaryBp.end,
-            strand: primaryBp.strand,
-            mateDirection: tickDirection(primaryBp.strand, !flip),
+            ...primary,
             name: row.FusionName,
             score: row.JunctionReadCount ? +row.JunctionReadCount : undefined,
             type: 'fusion',
-            mate: {
-                refName: mateBp.refName,
-                start: mateBp.start,
-                end: mateBp.end,
-                strand: mateBp.strand,
-                mateDirection: tickDirection(mateBp.strand, flip),
-            },
+            mate,
             ...row,
         });
     }

package/esm/StarFusionAdapter/configSchema.js

@@ -1,14 +1,13 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, fillLocations } from '@jbrowse/core/configuration';
 export function normalizeSnapshot(snap) {
     return snap.uri
-        ? {
-            ...snap,
+        ? fillLocations(snap, {
             starFusionLocation: {
                 uri: snap.uri,
                 baseUri: snap.baseUri,
                 locationType: 'UriLocation',
             },
-        }
+        })
         : snap;
 }
 /**

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "5.0.0-beta.3",
+  "version": "5.0.0-beta.7",
   "type": "module",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
@@ -27,7 +27,7 @@
     "@jbrowse/mobx-state-tree": "^6.5.1",
     "mobx": "^7.0.3",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.3"
+    "@jbrowse/core": "^5.0.0-beta.7"
   },
   "publishConfig": {
     "access": "public"